tbuckley/cabot-search huggingface dataset:
Abstract 2249: Development and validation of a pharmacodynamic (PD) assay for TOS-358, the first covalent inhibitor of PI3Kα in clinical development
Authors: John R. MacDougall, Raymond Mak, John Bradley, Allison Simpson, Claire May, Lan Wei, Kendra Ouellette, Marty Olbrot, Jimmy Blair, Neil Dhawan, Wei Chen
Journal: Cancer Research (2023)

Abstract TOS-358 is a first-in-class covalent inhibitor of PI3Kα and is currently in clinical development in a variety of solid malignancies. We have developed a fit-for-purpose pharmacodynamic assay to evaluate the target occupancy of TOS-358 in in vitro and in vivo setting at multiple timepoints. The PI3Kα assay allows direct measurement of both occupied and total protein in multiple different samples and tissue types. Signals of occupied and unoccupied PI3Kα proteins can be readily measured in cellular and in vivo samples. The assay was utilized in a large panel of cancer cell lines, revealing a direct correlation between target occupancy and pathway inhibition of markers such as phosphoAKT and phosphoS6. Critically, these correlations revealed the need to achieve near complete suppression of PI3Kα to enable sustained pathway inhibition and cancer cell death. We furthermore utilized this assay to explore the turnover rate of PI3Kα across multiple diverse tumor types, mutations, and tissues. This approach enables highly sensitive target engagement analysis of TOS-358 across multiple formats. Citation Format: John R. MacDougall, Raymond Mak, John Bradley, Allison Simpson, Claire May, Lan Wei, Kendra Ouellette, Marty Olbrot, Jimmy Blair, Neil Dhawan, Wei Chen. Development and validation of a pharmacodynamic (PD) assay for TOS-358, the first covalent inhibitor of PI3Kα in clinical development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2249.
Abstract 4853: Evaluating the role of melatonin in thyroid cancer cell (MDA-T41) apoptosis and metabolism modulation
Authors: Angela Huang, Daniel Sanches
Journal: Cancer Research (2023)

Abstract Melatonin, a hormone produced by the pineal gland, is typically known for its modulation of a number of physiological functions, alongside its ability to synchronize the sleep-wake rhythms. In recent years, however, its interactions with cancerous cells and role in prevention and treatment have been increasingly studied. It has been demonstrated that melatonin can improve the efficacy of chemotherapeutic drugs and directly inhibit tumorigenesis in experimental models of neoplasia. In addition, while melatonin typically displays anti-apoptotic effects in normal cells, it holds pro-apoptotic effects in cancer cells. Despite this, the mechanisms by which melatonin affects cell death and metabolism remain unclear due to the seeming difference from cell to cell. We aim to better understand the role of melatonin in regulating thyroid cancer cell apoptosis and metabolism. The MDA-T41 thyroid cancer cell line was cultured with varying quantities of melatonin. Steady volumes of staurosporine (an inductor of apoptotic cell death) were applied to cultures, and cell death levels were subsequently measured using the Realtime-Glo Annexin V Apoptosis and Necrosis assay. Our results showed that melatonin provided anti-apoptotic effects to MDA-T41 cells treated with staurosporine. Both apoptosis and necrosis were reduced by 50% in melatonin-treated cells 24 hours after staurosporine-induced cell death. Our next steps will be to evaluate the mechanisms and further signaling pathways involved in this apoptosis inhibition through Bcl-2 and p53 protein expression. Citation Format: Angela Huang, Daniel Sanches. Evaluating the role of melatonin in thyroid cancer cell (MDA-T41) apoptosis and metabolism modulation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4853.
Abstract 2814: The mutational basis of cancer's vulnerability to ionizing radiation
Authors: Priyanka Gopal, Mohamed E. Abazeed
Journal: Cancer Research (2023)

Abstract Introduction: Large-scale sequencing efforts have established that cancer-associated genetic alterations are highly diverse, posing a challenge to the identification of variants that regulate complex phenotypes like radiation sensitivity. The impact of the vast majority of rare or common genetic variants on the sensitivity of cancers to radiotherapy remains largely unknown. Methods: We developed a scalable gene editing and irradiation platform to assess the role of categories of variants in cells. Variants were prioritized based on genotype-phenotype associations from a previously completed large-scale cancer cell line radiation profiling study. Altogether, 488 alleles (396 unique SNVs) from 92 genes were generated and profiled in an immortalized lung cell line, BEAS-2B. We validated our results in other cell lines (TRT-HU1 and NCI-H520), in vivo via the use of both cell line and patient-derived murine xenografts, and in clinical cohorts. Results: We show that resistance to radiation is characterized by substantial inter- and intra-gene allelic variation. Some genes (e.g. KEAP1) demonstrated significant intragenic allelic variation in the magnitude of conferred resistance and other genes (e.g. CTNNB1) displayed both resistance and sensitivity in a protein domain-dependent manner. We combined results from our platform with gene expression and metabolite features and identified the upregulation of amino acid transporters that facilitate oxidative reductive capacity and cell cycle deregulation as key regulators of radiation sensitivity. Conclusions: Our results reveal new insights into the genetic determinants of tumor sensitivity to radiotherapy and nominate a multitude of cancer mutations that are predicted to impact treatment efficacy. Citation Format: Priyanka Gopal, Mohamed E. Abazeed. The mutational basis of cancer's vulnerability to ionizing radiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2814.
Abstract 108: Spatio-temporal view of malignant histogenesis and cancer evolution via formation of polyploid giant cancer cell
Authors: Xiaoran Li, Yanping Zhong, Xudong Zhang, Anil Sood, Jinsong Liu
Journal: Cancer Research (2023)

Abstract To understand how malignant tumors develop from single cells, we used long-term, time-lapse, live-cell imaging to track the dynamics of the cell membrane, nucleus, spindle, and cell cycle regulators during the development of high-grade, serous, carcinoma-derived organoids. Organoids are highly heterogeneous and include 2 major subtypes. Type-1 organoids are relatively homogeneous and develop via traditional mitosis, whereas type-2 organoids are highly heterogenous and are composed of differently sized polyploid giant cancer cells (PGCCs). Tracking the origin of PGCCs in type-2 organoids shows single cells first undergo asymmetric mitosis and nuclear fusion, followed by endoreplication, multipolar restitution mitosis, multipolar endomitosis, and karyokinesis. At the cellular level, the formation of PGCCs was associated with the formation of transient intracellular cells, termed fecundity cells. The fecundity cells underwent decellularization via the dissolution of the cell membrane, which allowed a giant nucleus to form via nuclear fusion. Different PGCCs underwent nuclear budding, decellularization, or entosis to form Russian doll-like tissue structures that facilitated rapid tumor growth and evolution. The uncoupling of nuclear augmentation from cytokinesis led to a rapid increase in the nuclear-to-cytoplasmic ratio and increased the genomic content of PGCCs, which facilitated macro-genomic evolution during tumor development. Our live-cell imaging evidence allows us to link nuclear replication and cancer evolution to the nuclear morphologies observed by pathologists under the microscope. PGCCs may be the central regulators of malignant histogenesis, cancer evolution, and physical barriers conferring resistance to immune therapy. Citation Format: Xiaoran Li, Yanping Zhong, Xudong Zhang, Anil Sood, Jinsong Liu. Spatio-temporal view of malignant histogenesis and cancer evolution via formation of polyploid giant cancer cell [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 108.
Abstract 4359: Interventions to improve pathologic nodal staging of curatively resected lung cancer: A population-based implementation study
Authors: Meredith A. Ray, Carrie Fehnel, Olawale Akinbobola, Andrea Saulsberry, Kourtney Dortch, Anberitha Matthews, Amal Anga, Christopher Giampapa, Elizabeth Sales, Sherry Okun, Edward T. Robbins, Bradley Wolf, Paul Levy, Horace L. Wiggins, Thomas Ng, Vishal Sachdev, Ganpat Valaulikar, Hetal D. Patel, Nicholas R. Faris, Matthew Smeltzer, Raymond U. Osarogiagbon
Journal: Cancer Research (2023)

Abstract Introduction. Despite its importance, pathologic nodal (pN) staging of lung cancer remains poor. We evaluated the quality and survival impact of two interventions to improve pN staging. Methods. Using a non-randomized stepped-wedge design, we implemented use of a lymph node (LN) specimen collection kit to improve intraoperative LN collection (surgical intervention) and a novel gross dissection method for intrapulmonary LN retrieval (pathology intervention) in 12 hospitals in five contiguous Hospital Referral Regions in AR, MS and TN (2009-2021). With appropriate statistical methods we compared surgical quality and survival of patients among: neither (Group 1), pathology only (Group 2), surgical only (Group 3), and both (Group 4) interventions. Results. Of 4,019 patients, 50%, 5%, 21% and 24%, were in Groups 1-4 respectively. Rates of non-examination of LNs and non-examination of mediastinal LNs: 11%, 9%, 0% and 0%; 29%, 35%, 2% and 2% respectively in Groups 1-4 (p&amp;lt;0.0001). Attainment of American College of Surgeons Operative Standard 5.8: 22%, 29%, 72%, 85%; International Association for the Study of Lung Cancer’s stringent definition of ‘complete resection’: 14%, 21%, 53%, 61% (p&amp;lt;0.0001). Compared to Group 1, adjusted hazard ratios, aHR (95% CI), were: Group 2, 0.93 (0.76-1.15); Group 3, 0.91 (0.78-1.03); Group 4, 0.75 (0.64-0.87). Compared to Group 2, Group 4 aHR- 0.72 (0.57-0.91); compared to Group 3, was 0.83 (0.69-0.99). These relationships remained after excluding wedge resections. Discussion. Combining a LN collection kit and novel gross dissection method significantly improved pN evaluation and survival in a population-based cohort. Citation Format: Meredith A. Ray, Carrie Fehnel, Olawale Akinbobola, Andrea Saulsberry, Kourtney Dortch, Anberitha Matthews, Amal Anga, Christopher Giampapa, Elizabeth Sales, Sherry Okun, Edward T. Robbins, Bradley Wolf, Paul Levy, Horace L. Wiggins, Thomas Ng, Vishal Sachdev, Ganpat Valaulikar, Hetal D. Patel, Nicholas R. Faris, Matthew Smeltzer, Raymond U. Osarogiagbon. Interventions to improve pathologic nodal staging of curatively resected lung cancer: A population-based implementation study. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4359.
Abstract 18: Transcriptomic analysis of mucinous adenocarcinoma in genetically-engineered mouse model
Authors: Haruki Sada, Hiroaki Niitsu, Hikaru Nakahara, Masashi Miguchi, Naoya Sakamoto, Naohide Oue, Hirotaka Tashiro, Hideki Ohdan, Takao Hinoi
Journal: Cancer Research (2023)

Abstract Background and Aim: The nature and characteristic of human mucinous colorectal adenocarcinomas have not been well elucidated yet. We previously reported a genetically-engineered mouse model for colonic neoplasia producing mucin based on inactivation of Transforming Growth Factor β Receptor Type II (Tgfbr2) and Apc (CDX2P-G19Cre;Apc flox/+;Tgfbr2flox/flox), which is useful to investigate the mechanism of tumor formation. This mouse model developed colonic neoplasia from 12 weeks of age. Despite the same genotype, 40% of the tumors were found mucinous adenocarcinoma and 28% were high-grade adenoma. For further investigation, we herein perform transcriptomic analysis to clarify the molecular differences in these two histologically different tumors. Method: Total RNA were extracted from mucinous adenocarcinomas and high-grade adenomas in CDX2P-G19Cre;Apcflox/+;Tgfbr2 flox/flox mice from fresh frozen tumors (n=3, each). Then, RNA-seq and Gene Set Enrichment Analysis were performed. Samples were sequenced on NovaSeq 6000, and gene sets queried included the Hallmark. Results: Mucinous adenocarcinoma and high-grade dysplasia were differentially clustered in principal component analysis despite the same genotype. Gene set enrichment analysis showed 19 upregulated signaling pathways including KRAS signaling and epithelial mesenchymal transition, and 8 suppressed signaling pathways including E2F targets and MYC targets in mucinous adenocarcinoma compared to high-grade dysplasia (FDR &amp;lt; 0.05). Conclusions: By comparing transcriptome of mucinous adenocarcinoma with high-grade adenoma in our mouse model, 27 differential signal pathways were detected. Some of these pathways are presumably associated with the nature and the characteristics of mucinous adenocarcinoma. We are further investigating the effects of these differences in signal pathways and the correlation with human mucinous adenocarcinoma. Citation Format: Haruki Sada, Hiroaki Niitsu, Hikaru Nakahara, Masashi Miguchi, Naoya Sakamoto, Naohide Oue, Hirotaka Tashiro, Hideki Ohdan, Takao Hinoi. Transcriptomic analysis of mucinous adenocarcinoma in genetically-engineered mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 18.
Abstract 5617: A novel DNA double-strand breaks biosensor based on fluorescence resonance energy transfer
Authors: Jung-Soo Suh, Tae-Jin Kim
Journal: Cancer Research (2023)

Abstract Revealing the spatiotemporal behavior of DNA double-strand breaks (DSBs) is crucial for understanding the processes of DNA damage and repair. Traditionally, γH2AX and DNA damage response (DDR) factors have been used to detect DSBs using classical biochemical assays, such as antibody-based immunostaining. However, a reliable method to visualize and assess DSB activity real-time in living cells is yet to be established. Herein, we developed a novel DNA double-strand breaks biosensor (DSBS) based on fluorescence resonance energy transfer (FRET) by employing the H2AX and BRCT1 domains. By applying FRET imaging with DSBS, we show that DSBS specifically reacts to drug- or ionizing radiation (IR)-induced γH2AX activity, allowing for the quantification of DSB events at high spatiotemporal resolutions. Taken together, we provide a new experimental tool to evaluate the spatiotemporal dynamics of DNA double-strand breaks in response to cancer therapies. Ultimately, our biosensor can be useful for elucidating the molecular mechanisms underlying DNA damage and repair processes and applying for cancer therapies. Citation Format: Jung-Soo Suh, Tae-Jin Kim. A novel DNA double-strand breaks biosensor based on fluorescence resonance energy transfer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5617.
Abstract 2996: CT26 neoantigen presentation and immunogenicity
Authors: Seeta Nyayapathy, Richard Jones, Michael Ford, Micah Doty, Julie M. Rumble
Journal: Cancer Research (2023)

Abstract The foundation of personalized cancer therapy is teaching a patient’s own immune system to directly kill the cancer cells. Vaccination against tumor antigens is one method being explored to generate immune responses against tumors, and may be particularly effective in conjunction with therapies currently in the clinic, such as checkpoint inhibition. Identification of antigens for use in a vaccine is the pinch point of this method, and many algorithms have been developed in an attempt to predict what epitopes will be both presented and immunogenic. Importantly, both public (common to multiple individuals/cancer types) and private (single individual) epitopes may contribute to the development of effective vaccines. Experimental identification of presented and immunogenic epitopes is crucial to building effective anti-cancer vaccines. Using immunopeptidome profiling, we have narrowed a collection of published potential neoantigens to those which were presented by MHC class I in the CT26 mouse colorectal cancer cell line. These peptides were synthesized and used to immunize BALB/c mice. The immunogenicity of the peptide mix was then evaluated by ELIspot to assess IFN-gamma responses in immunized mice. These experiments support a complete workflow for selection of potential cancer neoantigens which experimentally exhibit both MHC presentation and immunogenicity. Citation Format: Seeta Nyayapathy, Richard Jones, Michael Ford, Micah Doty, Julie M. Rumble. CT26 neoantigen presentation and immunogenicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2996.
Abstract 3525: VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis
Authors: Sarah Watson, Collette A. LaVigne, Lin Xu, Didier Surdez, Joanna Cyrta, Delia Calderon, Matthew V. Cannon, Matthew R. Kent, Katherine M. Silvius, Jack P. Kucinski, Emma N. Harrison, Whitney Murchison, Dinesh Rakheja, Franck Tirode, Olivier Delattre, James F. Amatruda, Genevieve C. Kendall
Journal: Cancer Research (2023)

Abstract Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that have not been functionally validated for their transformation capacity and biological activity. An example is the new fusion of transcriptional coactivators, VGLL2-NCOA2, found in infantile rhabdomyosarcoma. To delineate VGLL2-NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities, we implemented a cross-species comparative oncology approach with zebrafish, mouse allograft, and patient samples. We found that in our transgenic zebrafish and mouse allograft models, VGLL2-NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle. Zebrafish and mouse VGLL2-NCOA2 tumors are consistent with the human disease histologically and transcriptionally, and express diagnostic rhabdomyosarcoma markers. We found a shared molecular feature of these tumors was a suppression of myogenic differentiation pathways and reactivation of developmental programs. To identify impacted developmental programs, we transcriptionally clustered zebrafish VGLL2-NCOA2 tumors with the trajectory of early zebrafish development. A subset of VGLL2-NCOA2 zebrafish tumors cluster with embryonic somitogenesis and pinpoint VGLL2-NCOA2 developmental targets, including a RAS family GTPase, ARF6. In VGLL2-NCOA2 zebrafish, mouse allograft, and patient tumors, ARF6 is highly expressed and is absent from mature skeletal muscle. ARF6 knockout in our C2C12-VGLL2-NCOA2 cell culture model suppresses VGLL2-NCOA2 soft agar colony formation capacity, suggesting a genetic cooperating event in the disease. Our data indicate that VGLL2-NCOA2 is an oncogene which leverages developmental programs for tumorigenesis, and that the reactivation or persistence of ARF6 could represent a therapeutic opportunity. Citation Format: Sarah Watson, Collette A. LaVigne, Lin Xu, Didier Surdez, Joanna Cyrta, Delia Calderon, Matthew V. Cannon, Matthew R. Kent, Katherine M. Silvius, Jack P. Kucinski, Emma N. Harrison, Whitney Murchison, Dinesh Rakheja, Franck Tirode, Olivier Delattre, James F. Amatruda, Genevieve C. Kendall. VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3525.
Abstract 1650: Discovery of a novel Kevetrin analog as a potential therapeutic for ovarian cancer
Authors: Asif Raza, Jacek Krzeminski, Shantu Amin, Arun Sharma
Journal: Cancer Research (2023)

Abstract Kevetrin is an investigational new drug in phase I clinical trial on solid tumors (NCT01664000). It has shown its efficacy in various tumors, including lung, breast, colon, and ovarian cancer cell and xenograft models, both in a p53-dependent and -independent manner. In ovarian cancer cell lines with the TP53 mutation, p21 expression was found to be upregulated without the involvement of p53. Additionally, it was proposed that Kevetrin caused the histone deacetylase 6 (HDAC6) enzyme to be downregulated, negatively affecting the HDAC6-Hsp90 chaperone axis and causing the degradation of p53 in the mutant mice. In the present study, we designed and synthesized a novel analog (compound 900) of Kevetrin and its cytotoxicity was assessed using four different ovarian cancer cell lines viz. OVCAR-3, OVCAR-10, ES2, drug-resistant HeyA8 cells, and normal fibroblast cells (FHC). Compared to the control and Kevetrin, compound 900 inhibited the ovarian cancer cell viability in a dose- and time-dependent manner. The IC50 value of compound 900 was 0.8 μM, 0.7 μM, 0.8 μM, and 0.9 μM for OVCAR-3, HeyA8, OVCAR-10, and ES2 cells, respectively, while for Kevetrin the IC50 value was &amp;gt;100 μM for 48 h treatment. Compound 900 was thus found to be &amp;gt;100 times more potent than standard Kevetrin. To further acquaint the effect of 48 h treatment on cell proliferation, we performed trypan blue cell viability assay, trypan blue dye exclusion assay, Annexin V/7-AAD, Caspase 3/7 apoptosis assays, and Western blotting of apoptotic proteins involved in apoptosis. Compound 900 significantly induced apoptosis in OVCAR-3 and HeyA8 cells in a dose-dependent manner. Upregulation of several apoptotic proteins, as evident by Western blot, suggested that 900 causes the induction of apoptotic pathways efficiently. Further, the cell cycle analysis showed a significant arrest of OVCAR-3 and HeyA8 cells in the S-phase, which was further confirmed by the analysis of cyclin A2, cyclin-E1, p21, and p27 protein expression. Additionally, compound 900 caused a significant increase in the expression of the cell cycle inhibitory genes p21 and p27 in a p53-independent manner, compared to Kevetrin. Kevetrin has shown promise in preliminary clinical studies in solid tumor patients. The new analog 900 is &amp;gt;100 fold more potent than Kevetrin and holds great promise to be developed further for ovarian and other mechanistically relevant cancers. Citation Format: Asif Raza, Jacek Krzeminski, Shantu Amin, Arun Sharma. Discovery of a novel Kevetrin analog as a potential therapeutic for ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1650.